PMC:7143804 / 38489-43081 JSONTXT

{"target":"https://pubannotation.org/docs/sourcedb/PMC/sourceid/7143804","sourcedb":"PMC","sourceid":"7143804","source_url":"https://www.ncbi.nlm.nih.gov/pmc/7143804","text":"3.5. DNA Amplification\nFirst, to determine the temperature window of operation, MDA reactions are performed at 25 °C and 30 °C using the Illustra GenomiPhi V2 DNA amplification kit and EvaGreen fluorescence dye. From the literature, we know that this reaction does not work above 35 °C due to degradation of the protein activity in presence of a substrate [44]. In Figure 13, a graph of the fluorescence signal during MDA reactions at 25 °C and 30 °C, together with their non template control (NTC) is shown. These reactions are carried out in a conventional Bio-Rad CFX96 Touch Real-Time PCR machine (Bio-Rad Laboratories, Inc., Hercules, CA, USA) and the results show that the chosen proof-of-principle DNA amplification reaction is temperature dependent to some extent, but that there is a wide range of temperatures at which the amplification can be performed, i.e., 25°C to 35°C. This makes the functioning of the integrated resistive heater less critical than the stability shown in Figure 11c.\nMDA reactions are also performed inside an Eppendorf tube (Eppendorf AG, Hamburg, Germany) and inside the chip, again using the Illustra GenomiPhi V2 DNA amplification kit and EvaGreen fluorescence dye. As heat supply the water bath of an IKA Rotary Evaporator RV 8V (IKA-Werke, Staufen im Breisgau, Germany) is used. This water bath is according to its specification stable within a range of the set temperature ±0.1 °C. The chip and an Eppendorf tube are loaded with the reaction mixture containing the DNA sample and the EvaGreen dye solution. Here, the Eppendorf tube is serving as a control to show that the fabrication steps of the chips are not inhibiting the MDA reaction. The inlet and outlet of the chip are sealed with the Microseal “B” PCR plate sealing foil. The closed chip and tube are heated up in a separate water bath to 95 °C and kept at that temperature for 3 min to denaturate the dsDNA. Subsequently, the chip and tube are cooled down by placing it in an ice bath for 5 min after which the rest of the reagents are added. The complete mixtures are according to Table A3 in Appendix D. After closing the chip and tube again, they are placed in the water bath of the rotary evaporater and left there for 90 min, after which the reaction is terminated at 65 °C.\nThe MDA is also performed inside the chip, but with the integrated Au resistive heater serving as heat source. The set up shown schematically in Figure 12. The same procedure is followed as with the water bath heated test. Denaturation is done in a separate water bath. The heater is driven by an input potential of 3.2 V to get to a temperature of 30 °C and at the end of the reaction, the system is heated up to 65 °C by applying a potential of 9.2 V in order to terminate the amplification. In Figure 14 the logged temperature during the amplification is shown.\nAfter the amplifications, the reaction mixtures are pipetted out of the chips and tubes and into 1 mL quartz cuvettes containing 55 μL MilliQ DI water (Merck Millipore, Burlington, MA, USA). Fluorescence measurements are done in a Horiba Scientific FluoroMax+ spectrofluorometer to verify each amplification. The mixture is excitated at a wavelength of 500 nm and the emission spectrum is measured at wavelengths from 510 nm to 550 nm (bounded EvaGreen dye has a peak at 525 nm [63]). The measured spectra are normalized by subtracting the background signal of a mixture containing only the reaction buffer, the sample buffer, EvaGreen, and DNA. No Enzyme was added to this mixture, therefore no amplification could take place. See Figure 15 for the results obtained in the Eppendorf tube and chips. Figure A4 in Appendix E shows the background signal which is subtracted from all measurements.\nAs can be seen in Figure 15, the spectra of the amplification performed inside the chip, and by applying heat with the water bath as well as with the integrated Au-resistive heater, show the same trend as the amplification performed in the Eppendorf and heated by water bath. There is an order of magnitude difference in the fluorescence signal. However, the fluorescence intensity cannot be used as a value to quantify the amount of DNA. EvaGreen is a bis-intercalating cyanine fluorescence dye consisting of two monomeric DNA-binding dyes which are linked by a flexible spacer. These two DNA-binding dyes bind each in between two base pairs, which make them simple and fast, but also nonuniform and non-specific [44,63]. However, with this dye, a simple yes-or-no answer can be obtained if the amplification took place, as can be seen in Figure 15.","divisions":[{"label":"title","span":{"begin":0,"end":22}},{"label":"p","span":{"begin":23,"end":1000}},{"label":"p","span":{"begin":1001,"end":2281}},{"label":"p","span":{"begin":2282,"end":2846}},{"label":"p","span":{"begin":2847,"end":3741}}],"tracks":[{"project":"LitCovid-PubTator","denotations":[{"id":"270","span":{"begin":606,"end":609},"obj":"Gene"},{"id":"271","span":{"begin":563,"end":566},"obj":"Gene"},{"id":"277","span":{"begin":1223,"end":1228},"obj":"Chemical"},{"id":"278","span":{"begin":1324,"end":1329},"obj":"Chemical"},{"id":"279","span":{"begin":1525,"end":1533},"obj":"Chemical"},{"id":"280","span":{"begin":1826,"end":1831},"obj":"Chemical"},{"id":"281","span":{"begin":2170,"end":2175},"obj":"Chemical"},{"id":"285","span":{"begin":2349,"end":2351},"obj":"Chemical"},{"id":"286","span":{"begin":2481,"end":2486},"obj":"Chemical"},{"id":"287","span":{"begin":2540,"end":2545},"obj":"Chemical"},{"id":"290","span":{"begin":2979,"end":2981},"obj":"Gene"},{"id":"291","span":{"begin":2992,"end":2997},"obj":"Chemical"},{"id":"296","span":{"begin":3861,"end":3866},"obj":"Chemical"},{"id":"297","span":{"begin":3903,"end":3905},"obj":"Chemical"},{"id":"298","span":{"begin":4006,"end":4011},"obj":"Chemical"},{"id":"299","span":{"begin":4213,"end":4220},"obj":"Chemical"}],"attributes":[{"id":"A270","pred":"tao:has_database_id","subj":"270","obj":"Gene:6236"},{"id":"A271","pred":"tao:has_database_id","subj":"271","obj":"Gene:6236"},{"id":"A277","pred":"tao:has_database_id","subj":"277","obj":"MESH:D014867"},{"id":"A278","pred":"tao:has_database_id","subj":"278","obj":"MESH:D014867"},{"id":"A280","pred":"tao:has_database_id","subj":"280","obj":"MESH:D014867"},{"id":"A281","pred":"tao:has_database_id","subj":"281","obj":"MESH:D014867"},{"id":"A285","pred":"tao:has_database_id","subj":"285","obj":"MESH:D006046"},{"id":"A286","pred":"tao:has_database_id","subj":"286","obj":"MESH:D014867"},{"id":"A287","pred":"tao:has_database_id","subj":"287","obj":"MESH:D014867"},{"id":"A290","pred":"tao:has_database_id","subj":"290","obj":"Gene:4591"},{"id":"A291","pred":"tao:has_database_id","subj":"291","obj":"MESH:D014867"},{"id":"A296","pred":"tao:has_database_id","subj":"296","obj":"MESH:D014867"},{"id":"A297","pred":"tao:has_database_id","subj":"297","obj":"MESH:D006046"},{"id":"A298","pred":"tao:has_database_id","subj":"298","obj":"MESH:D014867"},{"subj":"270","pred":"source","obj":"LitCovid-PubTator"},{"subj":"271","pred":"source","obj":"LitCovid-PubTator"},{"subj":"277","pred":"source","obj":"LitCovid-PubTator"},{"subj":"278","pred":"source","obj":"LitCovid-PubTator"},{"subj":"279","pred":"source","obj":"LitCovid-PubTator"},{"subj":"280","pred":"source","obj":"LitCovid-PubTator"},{"subj":"281","pred":"source","obj":"LitCovid-PubTator"},{"subj":"285","pred":"source","obj":"LitCovid-PubTator"},{"subj":"286","pred":"source","obj":"LitCovid-PubTator"},{"subj":"287","pred":"source","obj":"LitCovid-PubTator"},{"subj":"290","pred":"source","obj":"LitCovid-PubTator"},{"subj":"291","pred":"source","obj":"LitCovid-PubTator"},{"subj":"296","pred":"source","obj":"LitCovid-PubTator"},{"subj":"297","pred":"source","obj":"LitCovid-PubTator"},{"subj":"298","pred":"source","obj":"LitCovid-PubTator"},{"subj":"299","pred":"source","obj":"LitCovid-PubTator"}],"namespaces":[{"prefix":"Tax","uri":"https://www.ncbi.nlm.nih.gov/taxonomy/"},{"prefix":"MESH","uri":"https://id.nlm.nih.gov/mesh/"},{"prefix":"Gene","uri":"https://www.ncbi.nlm.nih.gov/gene/"},{"prefix":"CVCL","uri":"https://web.expasy.org/cellosaurus/CVCL_"}]},{"project":"LitCovid-PD-FMA-UBERON","denotations":[{"id":"T58","span":{"begin":5,"end":8},"obj":"Body_part"},{"id":"T59","span":{"begin":156,"end":158},"obj":"Body_part"},{"id":"T61","span":{"begin":159,"end":162},"obj":"Body_part"},{"id":"T62","span":{"begin":312,"end":319},"obj":"Body_part"},{"id":"T63","span":{"begin":705,"end":708},"obj":"Body_part"},{"id":"T64","span":{"begin":1070,"end":1072},"obj":"Body_part"},{"id":"T65","span":{"begin":1148,"end":1150},"obj":"Body_part"},{"id":"T67","span":{"begin":1151,"end":1154},"obj":"Body_part"},{"id":"T68","span":{"begin":1506,"end":1509},"obj":"Body_part"},{"id":"T69","span":{"begin":2090,"end":2092},"obj":"Body_part"},{"id":"T70","span":{"begin":2096,"end":2104},"obj":"Body_part"},{"id":"T71","span":{"begin":3488,"end":3491},"obj":"Body_part"},{"id":"T72","span":{"begin":3660,"end":3668},"obj":"Body_part"},{"id":"T73","span":{"begin":4176,"end":4179},"obj":"Body_part"},{"id":"T74","span":{"begin":4266,"end":4269},"obj":"Body_part"},{"id":"T75","span":{"begin":4332,"end":4335},"obj":"Body_part"}],"attributes":[{"id":"A58","pred":"fma_id","subj":"T58","obj":"http://purl.org/sig/ont/fma/fma74412"},{"id":"A59","pred":"fma_id","subj":"T59","obj":"http://purl.org/sig/ont/fma/fma13443"},{"id":"A60","pred":"fma_id","subj":"T59","obj":"http://purl.org/sig/ont/fma/fma68615"},{"id":"A61","pred":"fma_id","subj":"T61","obj":"http://purl.org/sig/ont/fma/fma74412"},{"id":"A62","pred":"fma_id","subj":"T62","obj":"http://purl.org/sig/ont/fma/fma67257"},{"id":"A63","pred":"fma_id","subj":"T63","obj":"http://purl.org/sig/ont/fma/fma74412"},{"id":"A64","pred":"fma_id","subj":"T64","obj":"http://purl.org/sig/ont/fma/fma61898"},{"id":"A65","pred":"fma_id","subj":"T65","obj":"http://purl.org/sig/ont/fma/fma13443"},{"id":"A66","pred":"fma_id","subj":"T65","obj":"http://purl.org/sig/ont/fma/fma68615"},{"id":"A67","pred":"fma_id","subj":"T67","obj":"http://purl.org/sig/ont/fma/fma74412"},{"id":"A68","pred":"fma_id","subj":"T68","obj":"http://purl.org/sig/ont/fma/fma74412"},{"id":"A69","pred":"fma_id","subj":"T69","obj":"http://purl.org/sig/ont/fma/fma66599"},{"id":"A70","pred":"fma_id","subj":"T70","obj":"http://purl.org/sig/ont/fma/fma14542"},{"id":"A71","pred":"fma_id","subj":"T71","obj":"http://purl.org/sig/ont/fma/fma74412"},{"id":"A72","pred":"fma_id","subj":"T72","obj":"http://purl.org/sig/ont/fma/fma14542"},{"id":"A73","pred":"fma_id","subj":"T73","obj":"http://purl.org/sig/ont/fma/fma74412"},{"id":"A74","pred":"fma_id","subj":"T74","obj":"http://purl.org/sig/ont/fma/fma74412"},{"id":"A75","pred":"fma_id","subj":"T75","obj":"http://purl.org/sig/ont/fma/fma74412"},{"subj":"T58","pred":"source","obj":"LitCovid-PD-FMA-UBERON"},{"subj":"T59","pred":"source","obj":"LitCovid-PD-FMA-UBERON"},{"subj":"T61","pred":"source","obj":"LitCovid-PD-FMA-UBERON"},{"subj":"T62","pred":"source","obj":"LitCovid-PD-FMA-UBERON"},{"subj":"T63","pred":"source","obj":"LitCovid-PD-FMA-UBERON"},{"subj":"T64","pred":"source","obj":"LitCovid-PD-FMA-UBERON"},{"subj":"T65","pred":"source","obj":"LitCovid-PD-FMA-UBERON"},{"subj":"T67","pred":"source","obj":"LitCovid-PD-FMA-UBERON"},{"subj":"T68","pred":"source","obj":"LitCovid-PD-FMA-UBERON"},{"subj":"T69","pred":"source","obj":"LitCovid-PD-FMA-UBERON"},{"subj":"T70","pred":"source","obj":"LitCovid-PD-FMA-UBERON"},{"subj":"T71","pred":"source","obj":"LitCovid-PD-FMA-UBERON"},{"subj":"T72","pred":"source","obj":"LitCovid-PD-FMA-UBERON"},{"subj":"T73","pred":"source","obj":"LitCovid-PD-FMA-UBERON"},{"subj":"T74","pred":"source","obj":"LitCovid-PD-FMA-UBERON"},{"subj":"T75","pred":"source","obj":"LitCovid-PD-FMA-UBERON"}]},{"project":"LitCovid-PD-UBERON","denotations":[{"id":"T7","span":{"begin":1054,"end":1058},"obj":"Body_part"},{"id":"T8","span":{"begin":1449,"end":1453},"obj":"Body_part"},{"id":"T9","span":{"begin":1568,"end":1572},"obj":"Body_part"},{"id":"T10","span":{"begin":1793,"end":1797},"obj":"Body_part"},{"id":"T11","span":{"begin":1937,"end":1941},"obj":"Body_part"},{"id":"T12","span":{"begin":2135,"end":2139},"obj":"Body_part"},{"id":"T13","span":{"begin":3631,"end":3635},"obj":"Body_part"}],"attributes":[{"id":"A7","pred":"uberon_id","subj":"T7","obj":"http://purl.obolibrary.org/obo/UBERON_0000025"},{"id":"A8","pred":"uberon_id","subj":"T8","obj":"http://purl.obolibrary.org/obo/UBERON_0000025"},{"id":"A9","pred":"uberon_id","subj":"T9","obj":"http://purl.obolibrary.org/obo/UBERON_0000025"},{"id":"A10","pred":"uberon_id","subj":"T10","obj":"http://purl.obolibrary.org/obo/UBERON_0000025"},{"id":"A11","pred":"uberon_id","subj":"T11","obj":"http://purl.obolibrary.org/obo/UBERON_0000025"},{"id":"A12","pred":"uberon_id","subj":"T12","obj":"http://purl.obolibrary.org/obo/UBERON_0000025"},{"id":"A13","pred":"uberon_id","subj":"T13","obj":"http://purl.obolibrary.org/obo/UBERON_0000025"},{"subj":"T7","pred":"source","obj":"LitCovid-PD-UBERON"},{"subj":"T8","pred":"source","obj":"LitCovid-PD-UBERON"},{"subj":"T9","pred":"source","obj":"LitCovid-PD-UBERON"},{"subj":"T10","pred":"source","obj":"LitCovid-PD-UBERON"},{"subj":"T11","pred":"source","obj":"LitCovid-PD-UBERON"},{"subj":"T12","pred":"source","obj":"LitCovid-PD-UBERON"},{"subj":"T13","pred":"source","obj":"LitCovid-PD-UBERON"}]},{"project":"LitCovid-PD-MONDO","denotations":[{"id":"T35","span":{"begin":2989,"end":2991},"obj":"Disease"}],"attributes":[{"id":"A35","pred":"mondo_id","subj":"T35","obj":"http://purl.obolibrary.org/obo/MONDO_0018849"},{"subj":"T35","pred":"source","obj":"LitCovid-PD-MONDO"}]},{"project":"LitCovid-PD-CLO","denotations":[{"id":"T258","span":{"begin":280,"end":282},"obj":"http://purl.obolibrary.org/obo/CLO_0001000"},{"id":"T259","span":{"begin":320,"end":328},"obj":"http://purl.obolibrary.org/obo/CLO_0001658"},{"id":"T260","span":{"begin":344,"end":345},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T261","span":{"begin":376,"end":377},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T262","span":{"begin":404,"end":410},"obj":"http://purl.obolibrary.org/obo/SO_0000418"},{"id":"T263","span":{"begin":544,"end":545},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T264","span":{"begin":791,"end":792},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T265","span":{"begin":879,"end":881},"obj":"http://purl.obolibrary.org/obo/CLO_0001000"},{"id":"T266","span":{"begin":1054,"end":1058},"obj":"http://purl.obolibrary.org/obo/UBERON_0000025"},{"id":"T267","span":{"begin":1288,"end":1290},"obj":"http://purl.obolibrary.org/obo/UBERON_0003064"},{"id":"T268","span":{"begin":1383,"end":1384},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T269","span":{"begin":1449,"end":1453},"obj":"http://purl.obolibrary.org/obo/UBERON_0000025"},{"id":"T270","span":{"begin":1568,"end":1572},"obj":"http://purl.obolibrary.org/obo/UBERON_0000025"},{"id":"T271","span":{"begin":1587,"end":1588},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T272","span":{"begin":1746,"end":1747},"obj":"http://purl.obolibrary.org/obo/CLO_0001021"},{"id":"T273","span":{"begin":1793,"end":1797},"obj":"http://purl.obolibrary.org/obo/UBERON_0000025"},{"id":"T274","span":{"begin":1815,"end":1816},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T275","span":{"begin":1937,"end":1941},"obj":"http://purl.obolibrary.org/obo/UBERON_0000025"},{"id":"T276","span":{"begin":2090,"end":2092},"obj":"http://purl.obolibrary.org/obo/CLO_0001577"},{"id":"T277","span":{"begin":2135,"end":2139},"obj":"http://purl.obolibrary.org/obo/UBERON_0000025"},{"id":"T278","span":{"begin":2499,"end":2503},"obj":"http://purl.obolibrary.org/obo/UBERON_0000473"},{"id":"T279","span":{"begin":2529,"end":2530},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T280","span":{"begin":2614,"end":2615},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T281","span":{"begin":2714,"end":2715},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T282","span":{"begin":2929,"end":2934},"obj":"http://purl.obolibrary.org/obo/UBERON_0000025"},{"id":"T283","span":{"begin":3076,"end":3077},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T284","span":{"begin":3184,"end":3185},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T285","span":{"begin":3304,"end":3307},"obj":"http://purl.obolibrary.org/obo/CLO_0051582"},{"id":"T286","span":{"begin":3308,"end":3309},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T287","span":{"begin":3398,"end":3404},"obj":"http://purl.obolibrary.org/obo/SO_0000418"},{"id":"T288","span":{"begin":3408,"end":3409},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T289","span":{"begin":3631,"end":3635},"obj":"http://purl.obolibrary.org/obo/UBERON_0000025"},{"id":"T290","span":{"begin":3692,"end":3698},"obj":"http://purl.obolibrary.org/obo/SO_0000418"},{"id":"T291","span":{"begin":4080,"end":4086},"obj":"http://purl.obolibrary.org/obo/SO_0000418"},{"id":"T292","span":{"begin":4142,"end":4143},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T293","span":{"begin":4193,"end":4194},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T294","span":{"begin":4303,"end":4304},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"},{"id":"T295","span":{"begin":4489,"end":4490},"obj":"http://purl.obolibrary.org/obo/CLO_0001020"}],"attributes":[{"subj":"T258","pred":"source","obj":"LitCovid-PD-CLO"},{"subj":"T259","pred":"source","obj":"LitCovid-PD-CLO"},{"subj":"T260","pred":"source","obj":"LitCovid-PD-CLO"},{"subj":"T261","pred":"source","obj":"LitCovid-PD-CLO"},{"subj":"T262","pred":"source","obj":"LitCovid-PD-CLO"},{"subj":"T263","pred":"source","obj":"LitCovid-PD-CLO"},{"subj":"T264","pred":"source","obj":"LitCovid-PD-CLO"},{"subj":"T265","pred":"source","obj":"LitCovid-PD-CLO"},{"subj":"T266","pred":"source","obj":"LitCovid-PD-CLO"},{"subj":"T267","pred":"source","obj":"LitCovid-PD-CLO"},{"subj":"T268","pred":"source","obj":"LitCovid-PD-CLO"},{"subj":"T269","pred":"source","obj":"LitCovid-PD-CLO"},{"subj":"T270","pred":"source","obj":"LitCovid-PD-CLO"},{"subj":"T271","pred":"source","obj":"LitCovid-PD-CLO"},{"subj":"T272","pred":"source","obj":"LitCovid-PD-CLO"},{"subj":"T273","pred":"source","obj":"LitCovid-PD-CLO"},{"subj":"T274","pred":"source","obj":"LitCovid-PD-CLO"},{"subj":"T275","pred":"source","obj":"LitCovid-PD-CLO"},{"subj":"T276","pred":"source","obj":"LitCovid-PD-CLO"},{"subj":"T277","pred":"source","obj":"LitCovid-PD-CLO"},{"subj":"T278","pred":"source","obj":"LitCovid-PD-CLO"},{"subj":"T279","pred":"source","obj":"LitCovid-PD-CLO"},{"subj":"T280","pred":"source","obj":"LitCovid-PD-CLO"},{"subj":"T281","pred":"source","obj":"LitCovid-PD-CLO"},{"subj":"T282","pred":"source","obj":"LitCovid-PD-CLO"},{"subj":"T283","pred":"source","obj":"LitCovid-PD-CLO"},{"subj":"T284","pred":"source","obj":"LitCovid-PD-CLO"},{"subj":"T285","pred":"source","obj":"LitCovid-PD-CLO"},{"subj":"T286","pred":"source","obj":"LitCovid-PD-CLO"},{"subj":"T287","pred":"source","obj":"LitCovid-PD-CLO"},{"subj":"T288","pred":"source","obj":"LitCovid-PD-CLO"},{"subj":"T289","pred":"source","obj":"LitCovid-PD-CLO"},{"subj":"T290","pred":"source","obj":"LitCovid-PD-CLO"},{"subj":"T291","pred":"source","obj":"LitCovid-PD-CLO"},{"subj":"T292","pred":"source","obj":"LitCovid-PD-CLO"},{"subj":"T293","pred":"source","obj":"LitCovid-PD-CLO"},{"subj":"T294","pred":"source","obj":"LitCovid-PD-CLO"},{"subj":"T295","pred":"source","obj":"LitCovid-PD-CLO"}]},{"project":"LitCovid-PD-CHEBI","denotations":[{"id":"T238","span":{"begin":5,"end":8},"obj":"Chemical"},{"id":"T239","span":{"begin":80,"end":83},"obj":"Chemical"},{"id":"T240","span":{"begin":159,"end":162},"obj":"Chemical"},{"id":"T241","span":{"begin":207,"end":210},"obj":"Chemical"},{"id":"T242","span":{"begin":312,"end":319},"obj":"Chemical"},{"id":"T243","span":{"begin":418,"end":421},"obj":"Chemical"},{"id":"T244","span":{"begin":705,"end":708},"obj":"Chemical"},{"id":"T245","span":{"begin":1001,"end":1004},"obj":"Chemical"},{"id":"T246","span":{"begin":1070,"end":1072},"obj":"Chemical"},{"id":"T249","span":{"begin":1151,"end":1154},"obj":"Chemical"},{"id":"T250","span":{"begin":1199,"end":1202},"obj":"Chemical"},{"id":"T251","span":{"begin":1223,"end":1228},"obj":"Chemical"},{"id":"T252","span":{"begin":1262,"end":1264},"obj":"Chemical"},{"id":"T253","span":{"begin":1288,"end":1290},"obj":"Chemical"},{"id":"T254","span":{"begin":1324,"end":1329},"obj":"Chemical"},{"id":"T255","span":{"begin":1483,"end":1490},"obj":"Chemical"},{"id":"T256","span":{"begin":1506,"end":1509},"obj":"Chemical"},{"id":"T257","span":{"begin":1534,"end":1537},"obj":"Chemical"},{"id":"T258","span":{"begin":1538,"end":1546},"obj":"Chemical"},{"id":"T259","span":{"begin":1668,"end":1671},"obj":"Chemical"},{"id":"T260","span":{"begin":1826,"end":1831},"obj":"Chemical"},{"id":"T261","span":{"begin":2025,"end":2033},"obj":"Chemical"},{"id":"T262","span":{"begin":2170,"end":2175},"obj":"Chemical"},{"id":"T263","span":{"begin":2286,"end":2289},"obj":"Chemical"},{"id":"T264","span":{"begin":2349,"end":2351},"obj":"Chemical"},{"id":"T265","span":{"begin":2481,"end":2486},"obj":"Chemical"},{"id":"T266","span":{"begin":2540,"end":2545},"obj":"Chemical"},{"id":"T267","span":{"begin":2949,"end":2955},"obj":"Chemical"},{"id":"T268","span":{"begin":2992,"end":2997},"obj":"Chemical"},{"id":"T269","span":{"begin":3028,"end":3030},"obj":"Chemical"},{"id":"T272","span":{"begin":3160,"end":3167},"obj":"Chemical"},{"id":"T273","span":{"begin":3300,"end":3303},"obj":"Chemical"},{"id":"T274","span":{"begin":3410,"end":3417},"obj":"Chemical"},{"id":"T275","span":{"begin":3447,"end":3453},"obj":"Chemical"},{"id":"T276","span":{"begin":3466,"end":3472},"obj":"Chemical"},{"id":"T277","span":{"begin":3488,"end":3491},"obj":"Chemical"},{"id":"T278","span":{"begin":3521,"end":3528},"obj":"Chemical"},{"id":"T279","span":{"begin":3861,"end":3866},"obj":"Chemical"},{"id":"T280","span":{"begin":3903,"end":3905},"obj":"Chemical"},{"id":"T281","span":{"begin":4006,"end":4011},"obj":"Chemical"},{"id":"T282","span":{"begin":4176,"end":4179},"obj":"Chemical"},{"id":"T283","span":{"begin":4234,"end":4237},"obj":"Chemical"},{"id":"T284","span":{"begin":4266,"end":4269},"obj":"Chemical"},{"id":"T285","span":{"begin":4278,"end":4282},"obj":"Chemical"},{"id":"T286","span":{"begin":4332,"end":4335},"obj":"Chemical"},{"id":"T287","span":{"begin":4344,"end":4348},"obj":"Chemical"},{"id":"T288","span":{"begin":4374,"end":4378},"obj":"Chemical"},{"id":"T289","span":{"begin":4484,"end":4487},"obj":"Chemical"}],"attributes":[{"id":"A238","pred":"chebi_id","subj":"T238","obj":"http://purl.obolibrary.org/obo/CHEBI_16991"},{"id":"A239","pred":"chebi_id","subj":"T239","obj":"http://purl.obolibrary.org/obo/CHEBI_566274"},{"id":"A240","pred":"chebi_id","subj":"T240","obj":"http://purl.obolibrary.org/obo/CHEBI_16991"},{"id":"A241","pred":"chebi_id","subj":"T241","obj":"http://purl.obolibrary.org/obo/CHEBI_37958"},{"id":"A242","pred":"chebi_id","subj":"T242","obj":"http://purl.obolibrary.org/obo/CHEBI_36080"},{"id":"A243","pred":"chebi_id","subj":"T243","obj":"http://purl.obolibrary.org/obo/CHEBI_566274"},{"id":"A244","pred":"chebi_id","subj":"T244","obj":"http://purl.obolibrary.org/obo/CHEBI_16991"},{"id":"A245","pred":"chebi_id","subj":"T245","obj":"http://purl.obolibrary.org/obo/CHEBI_566274"},{"id":"A246","pred":"chebi_id","subj":"T246","obj":"http://purl.obolibrary.org/obo/CHEBI_27569"},{"id":"A247","pred":"chebi_id","subj":"T246","obj":"http://purl.obolibrary.org/obo/CHEBI_40618"},{"id":"A248","pred":"chebi_id","subj":"T246","obj":"http://purl.obolibrary.org/obo/CHEBI_73757"},{"id":"A249","pred":"chebi_id","subj":"T249","obj":"http://purl.obolibrary.org/obo/CHEBI_16991"},{"id":"A250","pred":"chebi_id","subj":"T250","obj":"http://purl.obolibrary.org/obo/CHEBI_37958"},{"id":"A251","pred":"chebi_id","subj":"T251","obj":"http://purl.obolibrary.org/obo/CHEBI_15377"},{"id":"A252","pred":"chebi_id","subj":"T252","obj":"http://purl.obolibrary.org/obo/CHEBI_73823"},{"id":"A253","pred":"chebi_id","subj":"T253","obj":"http://purl.obolibrary.org/obo/CHEBI_30366"},{"id":"A254","pred":"chebi_id","subj":"T254","obj":"http://purl.obolibrary.org/obo/CHEBI_15377"},{"id":"A255","pred":"chebi_id","subj":"T255","obj":"http://purl.obolibrary.org/obo/CHEBI_60004"},{"id":"A256","pred":"chebi_id","subj":"T256","obj":"http://purl.obolibrary.org/obo/CHEBI_16991"},{"id":"A257","pred":"chebi_id","subj":"T257","obj":"http://purl.obolibrary.org/obo/CHEBI_37958"},{"id":"A258","pred":"chebi_id","subj":"T258","obj":"http://purl.obolibrary.org/obo/CHEBI_75958"},{"id":"A259","pred":"chebi_id","subj":"T259","obj":"http://purl.obolibrary.org/obo/CHEBI_566274"},{"id":"A260","pred":"chebi_id","subj":"T260","obj":"http://purl.obolibrary.org/obo/CHEBI_15377"},{"id":"A261","pred":"chebi_id","subj":"T261","obj":"http://purl.obolibrary.org/obo/CHEBI_33893"},{"id":"A262","pred":"chebi_id","subj":"T262","obj":"http://purl.obolibrary.org/obo/CHEBI_15377"},{"id":"A263","pred":"chebi_id","subj":"T263","obj":"http://purl.obolibrary.org/obo/CHEBI_566274"},{"id":"A264","pred":"chebi_id","subj":"T264","obj":"http://purl.obolibrary.org/obo/CHEBI_29287"},{"id":"A265","pred":"chebi_id","subj":"T265","obj":"http://purl.obolibrary.org/obo/CHEBI_15377"},{"id":"A266","pred":"chebi_id","subj":"T266","obj":"http://purl.obolibrary.org/obo/CHEBI_15377"},{"id":"A267","pred":"chebi_id","subj":"T267","obj":"http://purl.obolibrary.org/obo/CHEBI_46727"},{"id":"A268","pred":"chebi_id","subj":"T268","obj":"http://purl.obolibrary.org/obo/CHEBI_15377"},{"id":"A269","pred":"chebi_id","subj":"T269","obj":"http://purl.obolibrary.org/obo/CHEBI_474859"},{"id":"A270","pred":"chebi_id","subj":"T269","obj":"http://purl.obolibrary.org/obo/CHEBI_73610"},{"id":"A271","pred":"chebi_id","subj":"T269","obj":"http://purl.obolibrary.org/obo/CHEBI_90325"},{"id":"A272","pred":"chebi_id","subj":"T272","obj":"http://purl.obolibrary.org/obo/CHEBI_60004"},{"id":"A273","pred":"chebi_id","subj":"T273","obj":"http://purl.obolibrary.org/obo/CHEBI_37958"},{"id":"A274","pred":"chebi_id","subj":"T274","obj":"http://purl.obolibrary.org/obo/CHEBI_60004"},{"id":"A275","pred":"chebi_id","subj":"T275","obj":"http://purl.obolibrary.org/obo/CHEBI_35225"},{"id":"A276","pred":"chebi_id","subj":"T276","obj":"http://purl.obolibrary.org/obo/CHEBI_35225"},{"id":"A277","pred":"chebi_id","subj":"T277","obj":"http://purl.obolibrary.org/obo/CHEBI_16991"},{"id":"A278","pred":"chebi_id","subj":"T278","obj":"http://purl.obolibrary.org/obo/CHEBI_60004"},{"id":"A279","pred":"chebi_id","subj":"T279","obj":"http://purl.obolibrary.org/obo/CHEBI_15377"},{"id":"A280","pred":"chebi_id","subj":"T280","obj":"http://purl.obolibrary.org/obo/CHEBI_29287"},{"id":"A281","pred":"chebi_id","subj":"T281","obj":"http://purl.obolibrary.org/obo/CHEBI_15377"},{"id":"A282","pred":"chebi_id","subj":"T282","obj":"http://purl.obolibrary.org/obo/CHEBI_16991"},{"id":"A283","pred":"chebi_id","subj":"T283","obj":"http://purl.obolibrary.org/obo/CHEBI_37958"},{"id":"A284","pred":"chebi_id","subj":"T284","obj":"http://purl.obolibrary.org/obo/CHEBI_16991"},{"id":"A285","pred":"chebi_id","subj":"T285","obj":"http://purl.obolibrary.org/obo/CHEBI_37958"},{"id":"A286","pred":"chebi_id","subj":"T286","obj":"http://purl.obolibrary.org/obo/CHEBI_16991"},{"id":"A287","pred":"chebi_id","subj":"T287","obj":"http://purl.obolibrary.org/obo/CHEBI_37958"},{"id":"A288","pred":"chebi_id","subj":"T288","obj":"http://purl.obolibrary.org/obo/CHEBI_22695"},{"id":"A289","pred":"chebi_id","subj":"T289","obj":"http://purl.obolibrary.org/obo/CHEBI_37958"},{"subj":"T238","pred":"source","obj":"LitCovid-PD-CHEBI"},{"subj":"T239","pred":"source","obj":"LitCovid-PD-CHEBI"},{"subj":"T240","pred":"source","obj":"LitCovid-PD-CHEBI"},{"subj":"T241","pred":"source","obj":"LitCovid-PD-CHEBI"},{"subj":"T242","pred":"source","obj":"LitCovid-PD-CHEBI"},{"subj":"T243","pred":"source","obj":"LitCovid-PD-CHEBI"},{"subj":"T244","pred":"source","obj":"LitCovid-PD-CHEBI"},{"subj":"T245","pred":"source","obj":"LitCovid-PD-CHEBI"},{"subj":"T246","pred":"source","obj":"LitCovid-PD-CHEBI"},{"subj":"T249","pred":"source","obj":"LitCovid-PD-CHEBI"},{"subj":"T250","pred":"source","obj":"LitCovid-PD-CHEBI"},{"subj":"T251","pred":"source","obj":"LitCovid-PD-CHEBI"},{"subj":"T252","pred":"source","obj":"LitCovid-PD-CHEBI"},{"subj":"T253","pred":"source","obj":"LitCovid-PD-CHEBI"},{"subj":"T254","pred":"source","obj":"LitCovid-PD-CHEBI"},{"subj":"T255","pred":"source","obj":"LitCovid-PD-CHEBI"},{"subj":"T256","pred":"source","obj":"LitCovid-PD-CHEBI"},{"subj":"T257","pred":"source","obj":"LitCovid-PD-CHEBI"},{"subj":"T258","pred":"source","obj":"LitCovid-PD-CHEBI"},{"subj":"T259","pred":"source","obj":"LitCovid-PD-CHEBI"},{"subj":"T260","pred":"source","obj":"LitCovid-PD-CHEBI"},{"subj":"T261","pred":"source","obj":"LitCovid-PD-CHEBI"},{"subj":"T262","pred":"source","obj":"LitCovid-PD-CHEBI"},{"subj":"T263","pred":"source","obj":"LitCovid-PD-CHEBI"},{"subj":"T264","pred":"source","obj":"LitCovid-PD-CHEBI"},{"subj":"T265","pred":"source","obj":"LitCovid-PD-CHEBI"},{"subj":"T266","pred":"source","obj":"LitCovid-PD-CHEBI"},{"subj":"T267","pred":"source","obj":"LitCovid-PD-CHEBI"},{"subj":"T268","pred":"source","obj":"LitCovid-PD-CHEBI"},{"subj":"T269","pred":"source","obj":"LitCovid-PD-CHEBI"},{"subj":"T272","pred":"source","obj":"LitCovid-PD-CHEBI"},{"subj":"T273","pred":"source","obj":"LitCovid-PD-CHEBI"},{"subj":"T274","pred":"source","obj":"LitCovid-PD-CHEBI"},{"subj":"T275","pred":"source","obj":"LitCovid-PD-CHEBI"},{"subj":"T276","pred":"source","obj":"LitCovid-PD-CHEBI"},{"subj":"T277","pred":"source","obj":"LitCovid-PD-CHEBI"},{"subj":"T278","pred":"source","obj":"LitCovid-PD-CHEBI"},{"subj":"T279","pred":"source","obj":"LitCovid-PD-CHEBI"},{"subj":"T280","pred":"source","obj":"LitCovid-PD-CHEBI"},{"subj":"T281","pred":"source","obj":"LitCovid-PD-CHEBI"},{"subj":"T282","pred":"source","obj":"LitCovid-PD-CHEBI"},{"subj":"T283","pred":"source","obj":"LitCovid-PD-CHEBI"},{"subj":"T284","pred":"source","obj":"LitCovid-PD-CHEBI"},{"subj":"T285","pred":"source","obj":"LitCovid-PD-CHEBI"},{"subj":"T286","pred":"source","obj":"LitCovid-PD-CHEBI"},{"subj":"T287","pred":"source","obj":"LitCovid-PD-CHEBI"},{"subj":"T288","pred":"source","obj":"LitCovid-PD-CHEBI"},{"subj":"T289","pred":"source","obj":"LitCovid-PD-CHEBI"}]},{"project":"LitCovid-PD-GO-BP","denotations":[{"id":"T12","span":{"begin":5,"end":22},"obj":"http://purl.obolibrary.org/obo/GO_0006277"},{"id":"T13","span":{"begin":159,"end":176},"obj":"http://purl.obolibrary.org/obo/GO_0006277"},{"id":"T14","span":{"begin":293,"end":304},"obj":"http://purl.obolibrary.org/obo/GO_0009056"},{"id":"T15","span":{"begin":705,"end":722},"obj":"http://purl.obolibrary.org/obo/GO_0006277"},{"id":"T16","span":{"begin":1151,"end":1168},"obj":"http://purl.obolibrary.org/obo/GO_0006277"}],"attributes":[{"subj":"T12","pred":"source","obj":"LitCovid-PD-GO-BP"},{"subj":"T13","pred":"source","obj":"LitCovid-PD-GO-BP"},{"subj":"T14","pred":"source","obj":"LitCovid-PD-GO-BP"},{"subj":"T15","pred":"source","obj":"LitCovid-PD-GO-BP"},{"subj":"T16","pred":"source","obj":"LitCovid-PD-GO-BP"}]},{"project":"LitCovid-sentences","denotations":[{"id":"T298","span":{"begin":0,"end":4},"obj":"Sentence"},{"id":"T299","span":{"begin":5,"end":22},"obj":"Sentence"},{"id":"T300","span":{"begin":23,"end":211},"obj":"Sentence"},{"id":"T301","span":{"begin":212,"end":361},"obj":"Sentence"},{"id":"T302","span":{"begin":362,"end":508},"obj":"Sentence"},{"id":"T303","span":{"begin":509,"end":884},"obj":"Sentence"},{"id":"T304","span":{"begin":885,"end":1000},"obj":"Sentence"},{"id":"T305","span":{"begin":1001,"end":1203},"obj":"Sentence"},{"id":"T306","span":{"begin":1204,"end":1318},"obj":"Sentence"},{"id":"T307","span":{"begin":1319,"end":1422},"obj":"Sentence"},{"id":"T308","span":{"begin":1423,"end":1547},"obj":"Sentence"},{"id":"T309","span":{"begin":1548,"end":1681},"obj":"Sentence"},{"id":"T310","span":{"begin":1682,"end":1772},"obj":"Sentence"},{"id":"T311","span":{"begin":1773,"end":1909},"obj":"Sentence"},{"id":"T312","span":{"begin":1910,"end":2044},"obj":"Sentence"},{"id":"T313","span":{"begin":2045,"end":2107},"obj":"Sentence"},{"id":"T314","span":{"begin":2108,"end":2281},"obj":"Sentence"},{"id":"T315","span":{"begin":2282,"end":2392},"obj":"Sentence"},{"id":"T316","span":{"begin":2393,"end":2437},"obj":"Sentence"},{"id":"T317","span":{"begin":2438,"end":2504},"obj":"Sentence"},{"id":"T318","span":{"begin":2505,"end":2551},"obj":"Sentence"},{"id":"T319","span":{"begin":2552,"end":2775},"obj":"Sentence"},{"id":"T320","span":{"begin":2776,"end":2846},"obj":"Sentence"},{"id":"T321","span":{"begin":2847,"end":3037},"obj":"Sentence"},{"id":"T322","span":{"begin":3038,"end":3155},"obj":"Sentence"},{"id":"T323","span":{"begin":3156,"end":3331},"obj":"Sentence"},{"id":"T324","span":{"begin":3332,"end":3492},"obj":"Sentence"},{"id":"T325","span":{"begin":3493,"end":3574},"obj":"Sentence"},{"id":"T326","span":{"begin":3575,"end":3646},"obj":"Sentence"},{"id":"T327","span":{"begin":3647,"end":3741},"obj":"Sentence"},{"id":"T328","span":{"begin":3742,"end":4017},"obj":"Sentence"},{"id":"T329","span":{"begin":4018,"end":4087},"obj":"Sentence"},{"id":"T330","span":{"begin":4088,"end":4180},"obj":"Sentence"},{"id":"T331","span":{"begin":4181,"end":4321},"obj":"Sentence"},{"id":"T332","span":{"begin":4322,"end":4464},"obj":"Sentence"},{"id":"T333","span":{"begin":4465,"end":4592},"obj":"Sentence"}],"namespaces":[{"prefix":"_base","uri":"http://pubannotation.org/ontology/tao.owl#"}],"attributes":[{"subj":"T298","pred":"source","obj":"LitCovid-sentences"},{"subj":"T299","pred":"source","obj":"LitCovid-sentences"},{"subj":"T300","pred":"source","obj":"LitCovid-sentences"},{"subj":"T301","pred":"source","obj":"LitCovid-sentences"},{"subj":"T302","pred":"source","obj":"LitCovid-sentences"},{"subj":"T303","pred":"source","obj":"LitCovid-sentences"},{"subj":"T304","pred":"source","obj":"LitCovid-sentences"},{"subj":"T305","pred":"source","obj":"LitCovid-sentences"},{"subj":"T306","pred":"source","obj":"LitCovid-sentences"},{"subj":"T307","pred":"source","obj":"LitCovid-sentences"},{"subj":"T308","pred":"source","obj":"LitCovid-sentences"},{"subj":"T309","pred":"source","obj":"LitCovid-sentences"},{"subj":"T310","pred":"source","obj":"LitCovid-sentences"},{"subj":"T311","pred":"source","obj":"LitCovid-sentences"},{"subj":"T312","pred":"source","obj":"LitCovid-sentences"},{"subj":"T313","pred":"source","obj":"LitCovid-sentences"},{"subj":"T314","pred":"source","obj":"LitCovid-sentences"},{"subj":"T315","pred":"source","obj":"LitCovid-sentences"},{"subj":"T316","pred":"source","obj":"LitCovid-sentences"},{"subj":"T317","pred":"source","obj":"LitCovid-sentences"},{"subj":"T318","pred":"source","obj":"LitCovid-sentences"},{"subj":"T319","pred":"source","obj":"LitCovid-sentences"},{"subj":"T320","pred":"source","obj":"LitCovid-sentences"},{"subj":"T321","pred":"source","obj":"LitCovid-sentences"},{"subj":"T322","pred":"source","obj":"LitCovid-sentences"},{"subj":"T323","pred":"source","obj":"LitCovid-sentences"},{"subj":"T324","pred":"source","obj":"LitCovid-sentences"},{"subj":"T325","pred":"source","obj":"LitCovid-sentences"},{"subj":"T326","pred":"source","obj":"LitCovid-sentences"},{"subj":"T327","pred":"source","obj":"LitCovid-sentences"},{"subj":"T328","pred":"source","obj":"LitCovid-sentences"},{"subj":"T329","pred":"source","obj":"LitCovid-sentences"},{"subj":"T330","pred":"source","obj":"LitCovid-sentences"},{"subj":"T331","pred":"source","obj":"LitCovid-sentences"},{"subj":"T332","pred":"source","obj":"LitCovid-sentences"},{"subj":"T333","pred":"source","obj":"LitCovid-sentences"}]}],"config":{"attribute types":[{"pred":"source","value type":"selection","values":[{"id":"LitCovid-PubTator","color":"#adec93","default":true},{"id":"LitCovid-PD-FMA-UBERON","color":"#ec93c7"},{"id":"LitCovid-PD-UBERON","color":"#93e1ec"},{"id":"LitCovid-PD-MONDO","color":"#ecdc93"},{"id":"LitCovid-PD-CLO","color":"#c293ec"},{"id":"LitCovid-PD-CHEBI","color":"#93eca8"},{"id":"LitCovid-PD-GO-BP","color":"#ec9397"},{"id":"LitCovid-sentences","color":"#93b1ec"}]}]}}